I have a pc with 2 500gb HDDs. I am currently running Windows 8.1 but am migrating to Ubuntu. I want to know how to setup the partitions during Installation, so that I would have Ubuntu installed on the first Hard Drive, with the whole system being there, while still being able to store random files in the second Hard Drive?

3 Answers
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You don't need to do anything special. Just start Ubuntu installation and select the option to erase everything and install Ubuntu. Your first hard disk will be selected automatically. The other one won't be used at all for the installation. It will keep all the partitions and the data it holds.

Like Stormlord said, when you do the installation it won't touch the second hard drive unless you explicitly allow it to. So make sure you don't accidentally approve writing over it! One thing of note, though (would have just commented on his answer but I don't have a high enough level yet), is that Linux and Windows tend towards different file systems. You should have an option during the installation (or immediately afterwards - Ubuntu has a nice program for partitions and file systems which you can use) to format the second hard drive into something more usable. Don't forget to back things up first!